Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1132 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg1215965939 sf1215963235 12 15965939 6.87E-184 4.34E-63
vg1215968758 sf1215966054 12 15968758 6.64E-183 2.68E-64
vg1210219854 sf1210217266 12 10219854 3.62E-93 1.37E-06
vg1210239280 sf1210236692 12 10239280 4.01E-88 3.78E-08
vg0621221946 sf0621220949 6 21221946 1.61E-84 3.48E-08
vg0217092666 sf0217086796 2 17092666 5.24E-82 NA
vg1224007541 sf1223973994 12 24007541 9.59E-82 NA
vg1221886540 sf1221853087 12 21886540 7.22E-79 1.97E-08
vg1215871396 sf1215868692 12 15871396 NA 5.95E-31
vg1215970855 sf1215968151 12 15970855 NA 4.82E-22
vg1215871822 sf1215869118 12 15871822 NA 7.22E-14
vg1216151894 sf1216149190 12 16151894 NA 2.38E-11
vg0610620315 sf0610619316 6 10620315 NA 9.02E-11
vg1104366840 sf1104362742 11 4366840 NA 2.13E-09
vg1216413575 sf1216410868 12 16413575 NA 2.64E-09
vg1216344388 sf1216341684 12 16344388 NA 3.07E-09
vg1216156576 sf1216153872 12 16156576 NA 1.03E-08
vg1212938220 sf1212935559 12 12938220 NA 1.09E-08
vg1216464142 sf1216461435 12 16464142 NA 1.21E-08
vg1216020887 sf1216018183 12 16020887 NA 1.44E-08
vg0521485463 sf0521422904 5 21485463 NA 1.64E-08
vg1216346285 sf1216343581 12 16346285 NA 1.65E-08
vg0920348485 sf0920348004 9 20348485 NA 2.37E-08
vg0401349008 sf0401344558 4 1349008 NA 5.29E-08
vg1216535261 sf1216532554 12 16535261 NA 1.18E-07
vg1215414598 sf1215411896 12 15414598 NA 2.43E-07
vg0616908094 sf0616907097 6 16908094 NA 2.48E-07
vg1219331439 sf1219302909 12 19331439 NA 3.91E-07